Sunday, February 26, 2012

Camels (and alpacas and equids)

There are camels, at least seven of them, in one of the vacant lots adjacent to the Institute. These (the lots, not the camels) are generally dominated by garbage-bespangled weeds and scrubby little trees. Today there is a circus truck, a tent with camel stalls, and a bunch of camels happily chomping the weeds down to the ground. I've seen goats, sheep and even cows used to clear brush, but the camels seem to be eating through the weeds faster than any of these could. The garbage has been removed (hopefully before the camels were let in), and there is a man who looks more like a circus worker than a government worker cutting and hauling away the woody stuff  the camels pass by (actually just throwing it into another one of the vacant lots). It seems like by tomorrow evening they will have to move them to another lot, or bring in fodder. I wonder if the circus is paying for, or being paid for, the use of the lot. Seems like a good deal for both parties.

It is 6C (43F) and sunny, which means that Rostockers think it is summer, and are walking around, admiring the camels. Some college kids have carried their couch onto the waterfront and are setting up a barbeque.  The ice on the harbor has all melted, and the gulls and mallards are looking for handouts.

Given all this, you might rightly ask why I am in the lab on a Sunday, instead of showing my daughter the camels, or walking with my wife, considering that I have excellent student assistants who are doing all of the actual lab work. The answer is that student assistants are not allowed to be in the lab by themselves, regardless of how mature or well trained they might be, or how routine or undangerous the work. So if the animals need to be checked every day, someone has to be here every day to baby-sit whichever student is in that day. This situation has actually gotten somewhat better. For 18 months that someone always had to be me, and I worked 7 days a week unless I was too sick and had to ask a colleague to cover for me. Now I am working with two wonderful post-docs, and only need to be in the lab every third weekend. Soon another graduate student will join us, and it will be every fourth weekend. Of course, the more experiments there are going on, the longer we have to be in the lab each day, and we are at about 6 hours now, and this will increase. So while those 7 day work weeks I was working included two pretty short days, the occasional work weekend will soon mean working almost full time.
This is honestly not so bad, but I’d rather be out watching the camels eat up that vacant lot.

Update: 10 camels, 6 alpacas, 4 miniature ponies, 3 donkeys and 9 horses. Only the camels are out grazing, fodder is being brought in and more tents are being set up in the areas already cleared.

Friday, February 24, 2012

National Academy of the Extremely Vigorous

People of higher educational attainment live longer. This is widely known. Somewhat less widely known is just how far up the attainment ladder this pattern goes. People with Master's Degrees tend to live longer than those who stop with a Bachelor's. Even more longevous, on the average, are those with doctorate. But people who get a doctorate and then go get some random job don't tend to live as long as those who become tenured professors. And sitting atop this hierarchy of attainment and longevity are the members of the elite scientific academies, such as the National Academies and the Royal Society. Many people's tendency when thinking about this correlation, between attainment and lifespan, is to assume that being better educated helps one live longer. To some extent this is certainly true, and at the level of primary education, and even college education, there is experimental evidence (both true experiments and accidental experiments through policy changes) to prove this. But in thinking about the differences between groups of people with graduate degrees, I rather suspect that the causal relationship is rather different.

I'm thinking about this at present because I have had a very productive evening. Since coming home from a full day at work I've made dinner, done the dishes, played with my daughter, rocked her to sleep, folded the laundry, done more laundry and folded that also, cleaned the cat's box, organized things around the house, rinsed the drop-cloth we put under the highchair while my daughter learns to eat, cleaned the broccoli and potato bits out of the bathtub, written work emails, taken down the garbage and the recycling, climbed the 18 flights of stairs to come back up and written half a blog post. This is extraordinary for me, especially this time of year. I am almost always either coming down with something or trying to recover from it, or coddling an inflamed joint, or just feeling low energy. I lose a disgusting amount of potential productivity to being sickly. The elite academies members I know, and those who are not yet in those academies but seem likely to be in them some day, are all people who are this energetic all the time. If they do get sick, they seem to almost always be back at in after a day or two. It is rare for me to recover from a cold in less than a week, and not rare for me to be out for two or three weeks at a stretch. This is not to say that many of these people are not also smarter than me in important respects, but the trait that most unifies the really successful academics I know is their extraordinary energy and vigor. My boss, nearing his 70th birthday, and a National Academy member, hardly seems to know what it is to feel tired. He'll attend meetings on four continents in the course of a week, say how exhausted he is, and still spring from his chair to scribble equations on his whiteboard. So my belief is that people of the highest academic attainment live longest not because they are of high attainment, but because they are remarkable in their health and energy, which also allows them to produce the torrent of great science necessary to be elected to one of these societies. Alright, enough writing, I'm exhausted.

Thursday, February 23, 2012

Scandal! Scientists find error in their own results!

Last September, a group of scientists in Italy got some strange results that made headlines around the world. Their results suggested that neutrinos were traveling faster than the speed of light.

I ask you to consider the following excerpt from a BBC article that came out just after their announcement:
"We tried to find all possible explanations for this," the report's author Antonio Ereditato of the Opera collaboration told BBC News on Thursday evening.
"We wanted to find a mistake - trivial mistakes, more complicated mistakes, or nasty effects - and we didn't.
"When you don't find anything, then you say 'well, now I'm forced to go out and ask the community to scrutinise this'."
Friday's meeting was designed to begin this process, with hopes that other scientists will find inconsistencies in the measurements and, hopefully, repeat the experiment elsewhere.
"Despite the large [statistical] significance of this measurement that you have seen and the stability of the analysis, since it has a potentially great impact on physics, this motivates the continuation of our studies in order to find still-unknown systematic effects," Dr Ereditato told the meeting.
"We look forward to independent measurement from other experiments."
I now ask you to consider the opening of NPR's article reporting the news that the error has probably been found:
Remember last year, when we reported that Italian scientists claimed to have broken the speed of light?

And this, from a blog post headed "That's Embarrassing" that one of my Facebook friends linked to:
Remember CERN's claim that they found neutrinos traveling faster than the speed of light? Weeeeeell now they want to renege, blaming a faulty fiber-optic cable and timing gear for the erroneous results. Jesus -- and we're supposed to trust these people to NOT tear open a black hole and swallow earth?
And this, linked to by another friend

Ridiculous: A Loose Cable Caused Those ‘Faster-Than-Light’ Particles

We know that Einstein always has the last laugh, but this is hilarious: the faster-than-light particles that could have wrecked his relativity theory are no more. It was a mistake in the test results caused by a loose cable.
Didn't anyone from the Genius Bar tell them about the first rule of tech support? Check your cables first! Oh, scientists!

I try not to get to whiny in complaining about the state of American science journalism, as I know it is not going to improve any time soon, but this really quite lamentable. The scientists involved were faced with data that could potentially destroy the theoretical underpinnings of their field. The wrong things to do would have been to ignore the data because they are theoretically heretical, or to make a big deal about their irrefutable and earthshaking discovery. Instead they did exactly what they should have done: They announce the situation to their peers and asked for help in evaluating the situation. They did this with full knowledge that their results would probably be shown to be in error, and that when that happened they would be mocked and insulted. This is an example of science working as it should, despite a dysfunctional press. No one, no matter how well established or well funded (or named Einstein), is the High Priest of science, and everyone's conclusions have to be reexamined and reconsidered. This responsibility to skepticism extends especially to one's own conclusions.

Their results have now been shown, by them, to have probably been an error, and the message the average American is getting is that these goofy Italian so-called-scientists were just too comical to even consider the possibility that Einstein was smarter than they are. NPR's science reporting is actually usually better than most, which is why I read their articles. In this case, they went with the invented scandal.

Tuesday, February 21, 2012

The boundries of personhood

A group of academics (psychologists, ethicist, biologists etc.) have recently endorsed a statement arguing that dolphins and whales do deserve the rights of humans, based on their intelligence, self-awareness, individuality, sociality and so forth.

 A curmudgeonly old man, who was an environmentalist but hated that he was because he didn't like to be associated with hippies, once opined to me as follows on this topic, only in much more colorful language: We can't start treating whales as though they have the same rights as humans, because if we give those rights to whales, we have to give them to apes too, and if we give them to apes pretty soon we'll be extending them to monkeys, and pretty soon antibiotics will be outlawed because they violate the inalienable rights of infectious bacteria.

I have mixed feelings about slippery slope arguments generally. Letting even minor instances of objectionable predilections (sexism, racism, etc.) slide really does seem to be a problem, on the principle that once people are used to these sentiments going unchallenged, they will feel freer to get more egregious. But we can and frequently do make different rules about the treatment of different categories of animals, and there is little likelihood of the rules that now apply to the study of chimpanzees being extended to include studies of bacteria, let alone infections. My research with live animals legally requires no review by any ethics board because I am working with invertebrates. Back when I studied birds, I needed committee approval just to go out in the woods and watch birds for scientific purposes, and my friends who study humans have sometimes had to get such approval just to reuse preexisting published and publicly available data on long-dead populations.

The fact of the matter is that we can and do make arbitrary decisions, often influenced by scientific knowledge but also influenced by emotional predilections, about who and what deserve what rights and protections. Before the US Civil War, southerners quibbled with the evidence that slaves were fully human, but more fundamentally they didn't admit that this implied that they deserved the same rights as other people. These days, American conservatives tend to want to extend the full rights of personhood to fetuses, embryos and potentially fertilized eggs. American liberals often want to extend these same rights to smart charismatic non-humans. Each side sees the other as both ridiculous and morally bankrupt. The difference underlying these wants are philosophical, moral, ethical and political, sometimes economic, but not generally founded in disagreements on scientific fact. Those factual disagreements usually follow, as each side looks for ways to justify its conclusions. I don't expect cetaceans will ever be granted the same rights as humans, but as we learn more about their mental and emotional lives, I do think it will become harder to treat them little different from large endangered fish. In other words, I think we will go part way down the slope.

Monday, February 20, 2012

Culturing culture

I am supervising/mentoring/collaborating with two post-doctoral researchers (a.k.a. postdocs), and greatly enjoying the process. They are both smart, hardworking and enthusiastic, and, unlike me, talented experimentalists. I am good at proposing experimental designs, and at inventing or improving upon experimental apparatus, but I managed to get through all my years of training as a biologist without ever being taught the nitty-gritty of laboratory work. I like to make things up as I go along, and work on twelve projects at a time, paying sporadic attention to each, and you can't really do experiments that way. But these two post-docs actually know what they are doing in the lab. It is impressive to see how thoroughly they train the students, how carefully they document their doings, and how well they know their organisms. As a grad student I started working with rotifers with almost no prior knowledge of rotifers, and without any advisor who knew rotifers. I read the literature, but there is a deep cultural knowledge about how to care for aquatic lab animals, with lore and practice around each group, and I had none of that. These two know, and it is wonderful to watch and learn.

Friday, February 17, 2012

I, flotsam.

Certain relatives of mine cling to the fantasy that I will be able to decide where I get a job, so as to live within a few miles of them. While the sentiment is appreciated, and shared, the reality is that I have almost no say in where I end up.

Let's review a few facts. First, the US economy is still in the shitter, if slightly less deep in than a few years ago. Lots of people, regardless of their industry, are moving wherever for whatever job they can get. Maybe there is some profession where you can just up and move where you want and be confident of making a living there, but I'm not sure what profession that would be at this point.

Second, even in good times, academics can almost never pick a city and get a job there. For hundreds of years academics have been moving to whatever University has a position for them. I'm reading a book about Alexander von Humboldt, who was one of the greatest scientists of the late 1700s and early 1800s, and even he keeps going from country to country looking for a patron and encountering academics working far from their own countries. There are extraordinarily few academics who can simply contact a University of interest and based on their scientific reputation be confident of getting a job there. Once you've won a Nobel Prize your chances are good. Barring that, good luck.

Third, I have done what most of the academic establishment says scientists should do, but very few fully do, because it makes publishing and job-hunting that much harder. My work is so damn interdisciplinary and specific that I am unlikely to fit the particular job description a small disciplinary department at a college or university is likely to write. I am on an email list for an online bulletin board for evolutionary biologists called EvolDir, and every few days I get an email for some position somewhere in the world that they are trying to fill. Here are a few of the most recent entry-level faculty positions:
•"There are several openings for Bioinformaticians and Software Developers at the University of Glasgow (UK)."
•The City University of New York seeks candidates with expertise "in tropical ecology, biogeography, evolutionary ecology, and conservation biology."
•" Tel Aviv University (ISRAEL) invites ... applicants who apply modern approaches to investigate fundamental problems in the general area of Plant Ecology. "
•UC Riverside "invites applications for a faculty position in plant evolutionary developmental biology."

These are positions I would bother applying for. This is not to say that I won't find anything, but rather that even if Near My Relatives U does decide to advertise for a new professor, they are more likely to be looking for an expert in the genomic analysis of primate fecal samples than they are a developmental evolutionary demographer. When I am ready to apply for positions, the question will not be, "Is that biking distance from my relatives?" but rather, "am I plausibly qualified for that position and is it a place where my wife is willing to live?" If it is, I'll need to apply. It is most likely that positions I do apply for will be among the relatively few broadly defined positions in evolutionary biology, with no further disciplinary restrictions. I very much approve of such broad-net casting, but it tends to lead to many hundreds of applications, as everyone in the field qualifies, so my chances with any one such position are slim.

If the economy were to improve dramatically, I could plausibly limit my search to within 1000 miles of my family. As it is, that limit will be about 12000 miles.

Wednesday, February 15, 2012

How I got stapled to a live turkey, and other fond memories of California

Round about this time of year I usually start making a list in my head of all the reasons I should probably not live in northern Germany much longer than necessary. One of my complaints is my general lack of opportunity to observe and interact with wildlife. I spent the better part of a decade doing biological field work, spending most of my time in the general proximity of wild animals. Sometimes it was more proximate than "general proximity" would suggest.

One day early in grad school, I was on my way into research museum where I worked, when I was stopped by the museum's eccentric old preparator, who was on his way out and wanted my help on I knew not what. I ended up on the beach with him and an armed National Park ranger using a carving knife to remove the head and fins of a dead whale that had washed up, for reasons that were not entirely explained to me at the time. I think the skull may have wound up in our museum's collection, but the ranger kept saying something about things not ending up on the black market.

Another time, my friend Alan wanted help catching and marking the wild turkeys he was studying. He would set up big walk-in traps baited with grain on cold mornings, and trap a whole flock of turkeys at a time. Then he would pull them out one at a time, measure them and attach a patagial tag to their wings. My job was to hold the birds' wings still while he attached the tag. Well it was quite cold and wet and my fingers were numb, so I didn't immediately notice that the rivet had gone not only through the bird's wing (as it was supposed to) but also into my hand. It took perhaps a minute to detach me from the turkey without further injuring either and bandage my hand before we could move on to the next turkey.

More often, my wildlife fix came in the form of bird-watching or lifting rocks to find lizards or salamanders. It was a rare week in California that I didn't get to do some wildlife viewing, and nature was as close as my back door. Here I live near the middle of a city with a long cold dark winter, and the life of a lab and desk biologist just isn't as adventurous. There is a city park across the street which in summer hosts some interesting if overfed animals, but especially this time of year I feel the absence of wildlife. Of course there is no guarantee that the next place I live will be so wild as is Berkeley (or preferably more so), but I can hope.

Sunday, February 12, 2012

Spanning the vastness

When I was but a lad, my siblings and I used to accuse my father of knowing everything, a charge he would always deny, observing that even excluding those things which are not known to anyone or are secret, and restricting ourselves to academic knowledge, there is more to know than any one person or any thousand people could possibly know.

To see why this is so, consider the sheer volume of scientific literature being produced. ISI Web of Knowledge, an online tool used primarily by scientists for finding scientific literature relevant to their work, indexes the contents of over 23,000 academic and scientific journals. Many lesser known, newer or otherwise less main-stream or traditional journals are not indexed at all. One needs to go to other databases to find information published in books, or in dissertations, or, or, or.

Like my father (as I am in most things), I find myself far too mortal to know any meaningful fraction of anything, even if we restrict ourselves just to academic biology. I'd say there are roughly 8000 peer-reviewed journals in which biological work is regularly published, and if you add up all the papers I skim through, it is probably the equivalent number of pages of the output of two or three of these. The papers I read in detail if assembled together would surely make up much less than the output of a single journal. And I put more time into reading and therefore less into writing than is optimal for my career.

One result of this is that I frequently find out that there exist thriving sub-disciplines of biology of which I have almost no knowledge. For example, only last week I for the first time heard the word "metabolomics." Google Scholar lists over 6000 papers in the last year on this rapidly expanding field about which I know no more than I could guess based on the name.

My knowledge of transcriptomics was quite as absent three years ago. Transcriptomics is the study of RNAs in the cell, generally in the context of gene expression patterns. I became interested in transcriptomics because I proposed that mortality risk during embryonic development would be highest at those stages at which gene expression patterns were changing fastest. I was a doctoral student at the time, and my adviser asked me if there was any way of testing this idea. I had to admit I didn't know if it was possible to test because I didn't know enough about the field I have since learned is called transcriptomics. The answer is that yes, there is a way of testing the idea, but it will cost a couple of hundred thousand dollars, and require collaboration with people who read different journals than I do. I will never be an expert in transcriptomics, but I can find a colleague who is, but has little knowledge of evolutionary demography, and invite him to collaborate on a project that combines our expertise. And this is why science can be a somewhat unified pursuit despite having far more product than one person can read even the titles of.  

I referred in my last post to one of my advisers at Berkeley, and one of my all around favorite human beings, Ron Lee. Ron would always advise me to think about my relative advantage, by which he meant I shouldn't just work on the most interesting or best questions, as there are far too many. Rather, I should choose among them by considering which questions I was better placed, given my strengths and resource, to answer than was anyone else likely to work on the question. Ron's advice has always served me well, and so I do consider this before starting any project. Frequently, as with this developmental transcriptomics and demography project, my relative advantage arises from the fact that I am combining two fields separated enough that no one else is likely to ask the question any time soon. Evolutionary demography and developmental biology do not, as a rule, talk to each other. Many fields of biology have almost no communication with each other, leaving vast unexplored interdisciplinary territories (unless that is all in some set of journals I haven't come across yet).

Saturday, February 11, 2012

Emissions of the aged

Projections of future carbon-dioxide emissions are complicated. How will energy consumption habits change as societies get richer or more urban? What mix of sources will we be getting our energy from?

My friend and colleague Emilo Zagheni decided we should make the calculus that much more complicated (and informative) by also asking how the aging of the population will influence carbon outputs. A demographer's demographer, which Emilio surely is, is never happy with any calculation that does not include age-structure in one way or another.

This article in the Economist summarizes what he did and what he found. As people get older, they tend to consume more and more, emitting more and more carbon, until 65ish, at which point consumption tends to start declining. See the graph, and the analysis, in the Economist, or the original in the journal Demography (2011) pp 371-399.  The punchline for the carbon-watcher is that the changing age-structure will tend to increase carbon emissions until about 2050, after which point such a large portion of the population will be above 65 (I'll be 73) that the age effect will begin to marginally decrease emissions.

I should finish with a quote from Ron Lee, Professor of both Demography and Economics at UC Berkeley, who both Emilio and I studied under. Ron was one of the inventors of the widely used Lee-Carter method* (1992) for forecasting future mortality patterns. Seventeen years later, I asked Ron how well his forecasts for the first 17 years matched what had actually happened in those years. He cocked his head slightly to the left, sighed sagely and said, "Well, demographers are well aware that our projections don't always fair so well in a complex world. But we console ourselves with the knowledge that we do much better than the economists."

* The original article has been cited more than 1000 times in the peer-reviewed literature, and modifications are used by the US Census Bureau, the UN, and so forth.

Friday, February 03, 2012

Suddenly crustaceans

I don't have a taxonomic specialization, and I'm happy with that. I've worked with or dug deeply in to the literature on hardwood forest trees, midges, several groups of birds, frogs, rotifers, primates and Hydra (the polyp, not the mythical beast). I've probably read more of the literature on beetles in the family Melyridae than any other non-entomologist who knows almost nothing about beetles.

I've now gotten to the point in my career where I am organizing a research group and serving on people's committees, and suddenly and unintentionally, I'm all into crustaceans. I'm supervising a post-doc and a doctoral student and on the committee of another student all working on different Daphnia projects. Daphnia are the model organism for crustaceans. I've got another post-doc working on barnacles (which despite their outward appearance as adults, are very much crustaceans, and go through not one but two amazing metamorphoses before ending up attached to ships, rocks or whales). This particular barnacle, Balanus improvisus was first described by Darwin (1854) in his giant book on barnacles that he wrote to procrastinate publishing On the Origin of Species (1859).

I've still got projects on Neurospora a fungus best known for ruining your bread, on Hydra, and on primates (including humans) going, but most of my time at the moment is crustacean focused. I suppose I will have to learn the basics of carcinology. Yes, that does come from the same root as carcinogen and carcinoma.


One of our laws in the U.S. requires that federal paperwork that people have to fill out be a bit longer than necessary in order to inform us that the federal government is mandated by law to reduce unnecessary paperwork, and to provide an estimate of how long it should take to deal with the particular piece of paperwork.

I'm preparing a grant application to the National Institutes of Health, and have spent the last month trying to figure out the rules, regulations and customs. They provide a helpful 264 page guide to filling out the application form, with links to more information online. This guide estimates it should take me 11 hours to prepare my application, not including the part where I design my research. It also advises me that I should read the whole guide, and the various additional information (including a very necessary glossary) before beginning to fill out the forms. A friend of mine, who recently looked at this instruction book and thereupon decided not to apply for NIH funds, suggested that anyone who could read and comprehend all 264+ pages in under 11 hours with enough time left to fill out the forms should probably just be acknowledged as a genius and given whatever money they need for their work.

I certainly don't blame NIH for having a lot of rules, or putting them in a book. They have a huge number of people asking them for money, the responsibility to make sure all the applications are dealt with fairly, and the need to comply with a very large number of laws on many topics. All sorts of special cases and exceptions arise, and they need to have guidance on everything (although I have already come across several places where one just has to know how it is done, generally by asking people who have done it before). So you can't really blame their helpful but understaffed staff. However the 11-hour estimate should probably be reexamined.

Anyway, I'm learning, and the next time I write an NIH application, it may take me only 11 hours to understand the rules, provided they haven't changed them too much. The sad part is that the proportion of applications funded continues to decline, even as the length of the application instructions increases. I'll distract myself from thinking about that by reading the 33 FAQs about the Modular Grant Application Concept.